init_site_models

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.

Richèl J.C. Bilderbeek

beautier

'BEAUti' from R

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Olivier Roy

Jana Riederer

init_site_models function

<dl><dt>site_models</dt>
<dd>one or more site models,
as returned by <code>create_site_model</code></dd>
<dt>ids</dt>
<dd>one or more alignments' IDs.
IDs can be extracted from their FASTA filenames
with <code>get_alignment_ids_from_fasta_filenames</code>)</dd>
<dt>distr_id</dt>
<dd>the first distributions' ID</dd>
<dt>param_id</dt>
<dd>the first parameter's ID</dd></dl>

Arguments

Author

Initializes all site models — init_site_models

<dl>

<dt>site_models</dt>
<dd>one or more site models,
as returned by <code>create_site_model</code></dd>


<dt>ids</dt>
<dd>one or more alignments' IDs.
IDs can be extracted from their FASTA filenames
with <code>get_alignment_ids_from_fasta_filenames</code>)</dd>


<dt>distr_id</dt>
<dd>the first distributions' ID</dd>


<dt>param_id</dt>
<dd>the first parameter's ID</dd>

</dl>

Initializes all site models

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init_site_models: Initializes all site models

Description

Usage

Value

Arguments

Author